Extending the models for XX and XO data, so as to keep a consensus network as far as possible.

Steps to find the common link to be added :
1.) Read in the extension.csv for both cell lines
2.) Remove links from TFs and Ligands
3.) Retain only links that have adjusted p-value < 0.01 and value !=0
4.) Calculate %improvement in residual for each cell line
5.) Find the intersection list,(Links that appear in both lists)
6.) Calculate the sum of %improvement in residual
7.) Order the intersection list by descending order of sum of %improvement in residual.
8.) Add the link with Max sum of %improvement to both models.

XX

Initial-Fit

Model residual = 2056

Link Extension :
adj_idx from to value residual df Res_delta df_delta pval adj_pval
1 178 Gsk3 Igfr 3.13276929030024 1280.86163056012 18 775.439838991864 2 0 0
2 171 Gsk3 Akt 2.00744510484014 1288.7198924196 18 767.581577132387 2 0 0
3 183 Gsk3 Pi3k 28.3512885413349 1289.13235441924 18 767.169115132742 2 0 0
4 176 Gsk3 Fgfr 0.191531853873651 1372.05906797687 18 684.242401575108 2 0 0
5 409 Stat3 Igfr 0.997104946770457 1503.11324672765 17 553.188222824328 1 0 0
6 220 Jak Igfr 0.0748374592692973 1503.11324675228 17 553.188222799702 1 0 0
7 407 Stat3 Fgfr 0.300461971006367 1515.31854390064 17 540.982925651346 1 0 0
8 218 Jak Fgfr 0.0226288712947294 1515.31854402861 17 540.982925523376 1 0 0
9 225 Jak Pi3k 0.694735352806384 1519.02257775189 17 537.278891800091 1 0 0
10 414 Stat3 Pi3k 9.22290789883903 1519.02257776675 17 537.278891785232 1 0 0
11 402 Stat3 Akt 0.536042655056134 1523.34265168251 17 532.958817869469 1 0 0
12 213 Jak Akt 0.0402569717690179 1523.34265168778 17 532.958817864204 1 0 0
13 92 Bmp4r Fgfr 10.0076490483583 1854.77447563085 18 201.526993921128 2 0 0
14 386 Smad2 Fgfr -2.41655006670941 1894.64741116463 17 161.65405838735 1 0 0
15 29 Actr Fgfr -0.792491707221983 1894.64741116818 17 161.654058383804 1 0 0
16 8 Activin Fgfr -0.792537854853646 1894.64741119847 17 161.654058353512 1 0 0
17 27 Actr Erk -0.753276971381174 1908.4536017862 17 147.847867765778 1 0 0
18 6 Activin Erk -0.753278094719914 1908.4536018017 17 147.847867750287 1 0 0
19 384 Smad2 Erk -2.29713833529869 1908.45360180763 17 147.847867744347 1 0 0
20 34 Actr Mek -0.179930950861247 1930.52896343579 17 125.772506116197 1 0 0

LA1:Jak -> Fgfr

Model residual = 1515

Link Extension :
adj_idx from to value residual df Res_delta df_delta pval adj_pval
1 178 Gsk3 Igfr 3.68714417419255 975.309714366926 19 539.692257816422 2 0 0
2 171 Gsk3 Akt 1.68295194837866 980.754743189037 19 534.24722899431 2 0 0
3 183 Gsk3 Pi3k 0.947852504056036 981.104896871733 19 533.897075311615 2 0 0
4 176 Gsk3 Fgfr 0.0366262460386825 1042.99093581945 19 472.011036363898 2 0 0
5 179 Gsk3 Jak 3.49480135093296 1186.00515889389 19 328.996813289455 2 0 0
6 180 Gsk3 Lifr 3.49479944763653 1186.0051589303 19 328.996813253044 2 0 0
7 92 Bmp4r Fgfr 0.137266584770296 1379.293214048 19 135.70875813535 2 0 0
8 95 Bmp4r Jak 10.0003396735026 1405.40002955712 19 109.601942626229 2 0 0
9 96 Bmp4r Lifr 1356.62829643212 1405.40002977268 19 109.601942410665 2 0 0
10 90 Bmp4r Erk 0.0999722355484721 1409.88137305731 19 105.120599126042 2 0 0
11 27 Actr Erk -0.615067412260236 1431.05413348414 18 83.9478386992096 1 0 0
12 6 Activin Erk -0.615070355453748 1431.05413349828 18 83.9478386850642 1 0 0
13 384 Smad2 Erk -1.87565732779727 1431.05413373099 18 83.9478384523607 1 0 0
14 97 Bmp4r Mek 0.0949591304987643 1432.52845600976 19 82.473516173585 2 0 0
15 100 Bmp4r Raf 0.0949591304987643 1432.52845600976 19 82.473516173585 2 0 0
16 101 Bmp4r Ras 0.0949591304987643 1432.52845600976 19 82.473516173585 2 0 0
17 409 Stat3 Igfr 7.7347392951796 1435.74300240161 18 79.2589697817409 1 0 0
18 220 Jak Igfr 0.376191899434823 1435.74303261976 18 79.258939563583 1 0 0
19 29 Actr Fgfr -0.183061257182024 1436.60116940374 18 78.4008027796108 1 0 0
20 8 Activin Fgfr -0.183060346059887 1436.60116941431 18 78.4008027690409 1 0 0

LA2:Gsk3->Igfr

Model residual = 971

Link Extension :
adj_idx from to value residual df Res_delta df_delta pval adj_pval
1 92 Bmp4r Fgfr 100.000000000035 840.631122580894 21 130.329009128159 2 0 0
2 90 Bmp4r Erk 99.9999999987995 866.335382828316 21 104.624748880737 2 0 0
3 96 Bmp4r Lifr 2.35528494640207 879.021008830448 21 91.9391228786054 2 0 0
4 95 Bmp4r Jak 100.000000009116 880.118790070241 21 90.8413416388127 2 0 0
5 6 Activin Erk -0.611024702426068 886.531262875663 20 84.4288688333903 1 0 0
6 27 Actr Erk -0.609450484425741 886.55941310913 20 84.4007185999238 1 0 0
7 97 Bmp4r Mek 99.9999999997936 890.523505991998 21 80.4366257170552 2 0 0
8 100 Bmp4r Raf 99.9999999997936 890.523505991998 21 80.4366257170552 2 0 0
9 101 Bmp4r Ras 99.9999999997936 890.523505991998 21 80.4366257170552 2 0 0
10 384 Smad2 Erk -1.25012097307715 890.830618123982 20 80.129513585072 1 0 0
11 213 Jak Akt 0.000419253601447264 901.164708669303 20 69.7954230397505 1 1.11022302462516e-16 3.7858605139718e-14
12 219 Jak Gsk3 0.00020314887762156 901.186098428986 20 69.7740332800676 1 1.11022302462516e-16 3.7858605139718e-14
13 402 Stat3 Akt 0.00135256498989191 901.187089844416 20 69.7730418646378 1 1.11022302462516e-16 3.7858605139718e-14
14 408 Stat3 Gsk3 0.000425516819558597 901.217903384329 20 69.7422283247242 1 1.11022302462516e-16 3.7858605139718e-14
15 409 Stat3 Igfr 0.000145276898279258 901.346403846118 20 69.6137278629359 1 1.11022302462516e-16 3.7858605139718e-14
16 220 Jak Igfr 0.000172377512952438 901.360783509842 20 69.5993481992116 1 1.11022302462516e-16 3.7858605139718e-14
17 225 Jak Pi3k 0.000127340116679159 901.430299565741 20 69.5298321433125 1 1.11022302462516e-16 3.7858605139718e-14
18 414 Stat3 Pi3k 0.000152008353737394 901.431073557295 20 69.5290581517581 1 1.11022302462516e-16 3.7858605139718e-14
19 415 Stat3 Raf -0.315097704393836 903.70022589935 20 67.2599058097031 1 2.22044604925031e-16 7.57172102794356e-14
20 416 Stat3 Ras -0.315097704663367 903.700225958777 20 67.2599057502767 1 2.22044604925031e-16 7.57172102794356e-14

LA3:Erk->Mek

Model residual = 932

Link Extension :
adj_idx from to value residual df Res_delta df_delta pval adj_pval
1 92 Bmp4r Fgfr 9.99999989258064 800.489508527619 22 131.646491603299 2 0 0
2 90 Bmp4r Erk 10.0000061725532 824.455100300836 22 107.680899830082 2 0 0
3 96 Bmp4r Lifr 2.44333632158931 839.394572423977 22 92.7414277069412 2 0 0
4 95 Bmp4r Jak 100.000000017537 840.213964306029 22 91.9220358248892 2 0 0
5 27 Actr Erk -0.787586097304015 845.537051106361 21 86.5989490245564 1 0 0
6 6 Activin Erk -0.788986702403185 845.572648952913 21 86.5633511780044 1 0 0
7 97 Bmp4r Mek 99.9999999997231 849.25343702957 22 82.8825631013473 2 0 0
8 100 Bmp4r Raf 99.9999999997231 849.25343702957 22 82.8825631013473 2 0 0
9 101 Bmp4r Ras 99.9999999997231 849.25343702957 22 82.8825631013473 2 0 0
10 384 Smad2 Erk -1.07203260647956 860.316271232803 21 71.8197288981145 1 0 0
11 391 Smad2 Mek -0.594094013606456 862.38978706802 21 69.7462130628979 1 1.11022302462516e-16 3.77475828372554e-14
12 395 Smad2 Ras -0.594094033003566 862.389787081142 21 69.7462130497757 1 1.11022302462516e-16 3.77475828372554e-14
13 394 Smad2 Raf -0.594094011724376 862.389787096731 21 69.746213034187 1 1.11022302462516e-16 3.77475828372554e-14
14 13 Activin Mek -0.196611026820534 862.476816638724 21 69.6591834921936 1 1.11022302462516e-16 3.77475828372554e-14
15 16 Activin Raf -0.196611026820534 862.476816638724 21 69.6591834921936 1 1.11022302462516e-16 3.77475828372554e-14
16 17 Activin Ras -0.196611029918045 862.476816661069 21 69.659183469849 1 1.11022302462516e-16 3.77475828372554e-14
17 34 Actr Mek -0.203517862423544 862.688904419659 21 69.4470957112586 1 1.11022302462516e-16 3.77475828372554e-14
18 38 Actr Ras -0.203517862423544 862.688904419659 21 69.4470957112586 1 1.11022302462516e-16 3.77475828372554e-14
19 37 Actr Raf -0.203517862425133 862.68890441968 21 69.4470957112377 1 1.11022302462516e-16 3.77475828372554e-14
20 213 Jak Akt 0.000365979200408284 863.85572187149 21 68.280278259428 1 1.11022302462516e-16 3.77475828372554e-14

LA4:Bmp4r->Fgfr

Model residual = 798

Link Extension :
adj_idx from to value residual df Res_delta df_delta pval adj_pval
1 408 Stat3 Gsk3 0.000275232994797559 738.147155832852 23 60.1464525852494 1 8.77076189453874e-15 2.97328828224863e-12
2 213 Jak Akt 0.000498128280588802 738.147716191157 23 60.1458922269441 1 8.77076189453874e-15 2.97328828224863e-12
3 402 Stat3 Akt 0.00171932617315295 738.193228654829 23 60.1003797632719 1 8.99280649946377e-15 3.04856140331822e-12
4 219 Jak Gsk3 0.000354679603965509 738.196248523367 23 60.0973598947348 1 8.99280649946377e-15 3.04856140331822e-12
5 220 Jak Igfr 0.000105246408657529 738.306015155016 23 59.9875932630858 1 9.54791801177635e-15 3.23674420599218e-12
6 409 Stat3 Igfr 0.000129314963713532 738.321226902665 23 59.9723815154364 1 9.65894031423886e-15 3.27438076652697e-12
7 225 Jak Pi3k 0.000236714658754552 738.350273655003 23 59.9433347630983 1 9.76996261670138e-15 3.31201732706177e-12
8 414 Stat3 Pi3k 0.000575541922563871 738.380943291085 23 59.9126651270159 1 9.88098491916389e-15 3.34965388759656e-12
9 227 Jak Ras -0.166748915696276 749.589351842409 23 48.7042565756926 1 2.97617486211266e-12 1.00892327825619e-09
10 223 Jak Mek -0.166748874957404 749.589360034352 23 48.7042483837498 1 2.97617486211266e-12 1.00892327825619e-09
11 226 Jak Raf -0.16674885028288 749.589365471779 23 48.7042429463228 1 2.97617486211266e-12 1.00892327825619e-09
12 317 Raf Actr 0.322276720958421 749.59906883644 23 48.6945395816618 1 2.99094082834017e-12 1.01392894080732e-09
13 355 Ras Smad2 0.322277616308061 749.599075847399 23 48.6945325707023 1 2.99094082834017e-12 1.01392894080732e-09
14 334 Raf Smad2 0.322277669996231 749.599076262919 23 48.6945321551824 1 2.99094082834017e-12 1.01392894080732e-09
15 338 Ras Actr 0.322277706849764 749.599078178269 23 48.6945302398328 1 2.99094082834017e-12 1.01392894080732e-09
16 149 Fgfr Actr 0.323904084271943 749.601092995369 23 48.692515422732 1 2.99404945280912e-12 1.01498276450229e-09
17 166 Fgfr Smad2 0.32390408433123 749.601092995999 23 48.6925154221021 1 2.99404945280912e-12 1.01498276450229e-09
18 27 Actr Erk -0.426069352335274 755.91483353031 23 42.3787748877913 1 7.52017337291022e-11 2.54933877341656e-08
19 6 Activin Erk -0.957783983564549 757.448642077237 23 40.8449663408646 1 1.64797175905562e-10 5.58662426319855e-08
20 384 Smad2 Erk -1.03133109305999 758.504227806685 23 39.7893806114159 1 2.82878942492459e-10 9.58959615049436e-08

LA5:Jak->Gsk3

Model residual = 738

Link Extension :
adj_idx from to value residual df Res_delta df_delta pval adj_pval
1 27 Actr Erk -0.72293860974715 676.169306265696 24 61.7711949347711 1 3.88578058618805e-15 1.31339383813156e-12
2 6 Activin Erk -0.993572104456671 681.66468775076 24 56.2758134497076 1 6.29496454962464e-14 2.12769801777313e-11
3 384 Smad2 Erk -1.00815609510703 689.978163230478 24 47.9623379699897 1 4.34485780687055e-12 1.46856193872225e-09
4 34 Actr Mek -0.166895406755719 691.240344479409 24 46.7001567210581 1 8.27227175648204e-12 2.79602785369093e-09
5 37 Actr Raf -0.166895406755719 691.240344479409 24 46.7001567210581 1 8.27227175648204e-12 2.79602785369093e-09
6 38 Actr Ras -0.166895406755719 691.240344479409 24 46.7001567210581 1 8.27227175648204e-12 2.79602785369093e-09
7 13 Activin Mek -0.170926272258106 692.032845749231 24 45.9076554512358 1 1.23960841591497e-11 4.1898764457926e-09
8 16 Activin Raf -0.170926272258106 692.032845749231 24 45.9076554512358 1 1.23960841591497e-11 4.1898764457926e-09
9 17 Activin Ras -0.170926272258106 692.032845749231 24 45.9076554512358 1 1.23960841591497e-11 4.1898764457926e-09
10 86 Bmp4r Actr 1.46213132226849 692.141349173648 24 45.7991520268189 1 1.31020749805089e-11 4.42850134341201e-09
11 103 Bmp4r Smad2 1.46203089405264 692.142403593777 24 45.7980976066898 1 1.3109069385564e-11 4.43086545232063e-09
12 5 Activin Bmp4r -0.673727432466445 697.219786782938 24 40.7207144175295 1 1.7561563314672e-10 5.93580840035914e-08
13 26 Actr Bmp4r -0.369203746740597 697.322620742319 24 40.6178804581481 1 1.85105042405098e-10 6.25655043329231e-08
14 29 Actr Fgfr -0.192327175159802 697.904213328672 24 40.0362878717949 1 2.4928847874861e-10 8.42595058170302e-08
15 8 Activin Fgfr -0.306525895162012 698.342846422195 24 39.5976547782723 1 3.12057824025658e-10 1.05475544520672e-07
16 383 Smad2 Bmp4r -1.00150976338793 698.417351527524 24 39.5231496729432 1 3.24193338840928e-10 1.09577348528234e-07
17 391 Smad2 Mek -0.980497187650536 702.631447958006 24 35.3090532424615 1 2.81321310691141e-09 9.50866030136057e-07
18 394 Smad2 Raf -0.980497187650536 702.631447958006 24 35.3090532424615 1 2.81321310691141e-09 9.50866030136057e-07
19 395 Smad2 Ras -0.980497187650479 702.631447958664 24 35.3090532418037 1 2.81321310691141e-09 9.50866030136057e-07
20 208 Igfr Smad2 0.251402223524026 703.799197742007 24 34.1413034584598 1 5.12517772666143e-09 1.73231007161156e-06

LA6:Bmp4r->Smad2

Model residual = 692

Link Extension :
adj_idx from to value residual df Res_delta df_delta pval adj_pval
1 6 Activin Erk -0.999162539749085 636.131302678366 25 55.7412262647932 1 8.27116153345742e-14 2.78738143677515e-11
2 394 Smad2 Raf -0.917124241774304 641.589286821836 25 50.2832421213229 1 1.33082433961818e-12 4.48487802451327e-10
3 27 Actr Erk -0.371797470550757 644.66350691414 25 47.2090220290194 1 6.38056274482324e-12 2.15024964500543e-09
4 37 Actr Raf -0.161981281597708 645.878577216417 25 45.9939517267425 1 1.18618448397001e-11 3.99744171097893e-09
5 38 Actr Ras -0.161981281597708 645.878577216417 25 45.9939517267425 1 1.18618448397001e-11 3.99744171097893e-09
6 34 Actr Mek -0.16197557293187 645.880509363129 25 45.9920195800304 1 1.18736132037611e-11 4.00140764966749e-09
7 8 Activin Fgfr -0.301001931622983 651.935719857307 25 39.9368090858525 1 2.62313060162001e-10 8.83995012745943e-08
8 29 Actr Fgfr -1.08636633192704 652.414723689582 25 39.4578052535772 1 3.35225180947418e-10 1.1297088597928e-07
9 384 Smad2 Erk -1.00016218012012 652.592232058965 25 39.2802968841949 1 3.6712732853772e-10 1.23721909717212e-07
10 13 Activin Mek -0.1 653.860220662579 25 38.0123082805802 1 7.02997438040143e-10 2.36910136619528e-07
11 16 Activin Raf -0.1 653.860220662579 25 38.0123082805802 1 7.02997438040143e-10 2.36910136619528e-07
12 17 Activin Ras -0.1 653.860220662579 25 38.0123082805802 1 7.02997438040143e-10 2.36910136619528e-07
13 5 Activin Bmp4r -0.999976327986681 659.036580110105 25 32.8359488330549 1 1.00273245262628e-08 3.37920836535056e-06
14 194 Igfr Bmp4r 8.75867295528011 660.382843487529 25 31.4896854556308 1 2.00502497937904e-08 6.75693418050736e-06
15 173 Gsk3 Bmp4r 7.97385173700289 662.907023443208 25 28.9655054999513 1 7.36786811561529e-08 2.48297155496235e-05
16 47 Akt Bmp4r 0.717958514203464 665.709742264527 25 26.1627866786328 1 3.13812181462758e-07 0.000105754705152949
17 383 Smad2 Bmp4r -9.99995486166114 666.566622214485 25 25.3059067286748 1 4.89208353160464e-07 0.000164863215015076
18 201 Igfr Lifr 1.75521212473151 667.546249096471 25 24.3262798466883 1 8.13219817707989e-07 0.000274055078567592
19 200 Igfr Jak 2.03708486202796 667.564188397286 25 24.3083405458739 1 8.20828729986012e-07 0.000276619282005286
20 54 Akt Lifr 0.672753595187013 667.58569830976 25 24.2868306333991 1 8.30046285371644e-07 0.000279725598170244

LA7:Actr->Ras

Model residual = 645

Link Extension :
adj_idx from to value residual df Res_delta df_delta pval adj_pval
1 116 Erk Jak 0.478092151777645 622.890849891522 26 22.1862135225255 1 2.47444245271566e-06 0.000831412664112462
2 117 Erk Lifr 0.47577560738498 622.908363089392 26 22.1687003246558 1 2.49711746791448e-06 0.000839031469219265
3 135 Fgf4 Gsk3 -2.71585656327465e-05 623.728585422478 26 21.3484779915697 1 3.82924638897553e-06 0.00128662678669578
4 136 Fgf4 Igfr -2.86536692384106e-05 623.731510901098 26 21.3455525129493 1 3.83509419543682e-06 0.00128859164966677
5 141 Fgf4 Pi3k -2.94781790313922e-05 623.732390155354 26 21.3446732586934 1 3.83685350779928e-06 0.00128918277862056
6 129 Fgf4 Akt -0.000297173859917682 623.74987659752 26 21.3271868165277 1 3.87201108298374e-06 0.00130099572388254
7 293 NoLif Stat3 -0.633083094709011 625.124078968803 26 19.9529844452446 1 7.9369968508658e-06 0.00266683094189091
8 54 Akt Lifr 1.13010959589657 625.348599860944 26 19.7284635531037 1 8.92619281955831e-06 0.00299920078737159
9 53 Akt Jak 1.1305206470739 625.38973354965 26 19.6873298643975 1 9.12040688494375e-06 0.0030644567133411
10 292 NoLif Smad2 -0.212124185477102 626.004676226597 26 19.0723871874505 1 1.25852688037664e-05 0.00422865031806551
11 110 Erk Bmp4r 0.665190083093769 626.174236478189 26 18.9028269358583 1 1.37548687854094e-05 0.00462163591189756
12 263 Mek Jak 1.00112015417932 626.311279040538 26 18.7657843735101 1 1.47795007953144e-05 0.00496591226722564
13 240 Lifr Gsk3 0.00656006894227856 626.371419277829 26 18.7056441362183 1 1.52530331597456e-05 0.00512501914167452
14 282 NoLif Gsk3 0.00618796299929441 626.372558183071 26 18.7045052309766 1 1.5262146185191e-05 0.00512808111822418
15 234 Lifr Akt 0.0050438521289888 626.409471590698 26 18.6675918233497 1 1.55604909786167e-05 0.00522832496881521
16 276 NoLif Akt 0.00479654260789317 626.41251001061 26 18.6645534034375 1 1.55853077490331e-05 0.00523666340367512
17 215 Jak Bmp4r 0.118761187021543 626.42147542289 26 18.6555879911574 1 1.56587661087615e-05 0.00526134541254386
18 246 Lifr Pi3k 0.000377337007281183 626.645679302902 26 18.4313841111457 1 1.76133060604267e-05 0.00591807083630337
19 288 NoLif Pi3k 0.000635751026862691 626.652980261552 26 18.4240831524957 1 1.76809178989989e-05 0.00594078841406363
20 314 Pi3k Stat3 0.246120924039924 626.822103850259 26 18.2549595637889 1 1.93222196843701e-05 0.00649226581394835

LA8:Gsk3->Stat3

Model residual = 627

Link Extension :
adj_idx from to value residual df Res_delta df_delta pval adj_pval
1 240 Lifr Gsk3 0.0123762772846946 603.698920221329 27 23.1442463148313 1 1.502922328811e-06 0.000503478980151685
2 136 Fgf4 Igfr -0.000463530799485467 604.436180398655 27 22.4069861375052 1 2.20570240327955e-06 0.000738910305098649
3 141 Fgf4 Pi3k -7.33729677965211e-05 604.479663799603 27 22.3635027365569 1 2.25621130800491e-06 0.000755830788181645
4 129 Fgf4 Akt -0.00048410935365824 604.517974631944 27 22.3251919042166 1 2.30167259429592e-06 0.000771060319089133
5 135 Fgf4 Gsk3 -2.43370532758539e-05 604.637065005766 27 22.2061015303938 1 2.44894304779475e-06 0.000820395921011241
6 282 NoLif Gsk3 0.00176389229399893 606.007911035068 27 20.8352555010919 1 5.00530618852135e-06 0.00167677757315465
7 292 NoLif Smad2 -0.211558679593845 607.729688381208 27 19.1134781549518 1 1.23171971074809e-05 0.0041262610310061
8 250 Lifr Smad2 -0.211558680003902 607.729688477853 27 19.1134780583074 1 1.23171977312042e-05 0.00412626123995341
9 246 Lifr Pi3k 0.0012827875580377 608.433015651597 27 18.4101508845628 1 1.78106644715958e-05 0.00596657259798459
10 288 NoLif Pi3k 0.000592858882894678 608.442322227469 27 18.4008443086908 1 1.78978659048923e-05 0.00599578507813892
11 404 Stat3 Bmp4r 0.0442503451274059 609.070914378897 27 17.7722521572631 1 2.48988152556917e-05 0.00834110311065672
12 403 Stat3 Bmp4 1 609.984942067667 27 16.8582244684928 1 4.02784089119645e-05 0.0134932669855081
13 418 Stat3 Smad2 0.133507704576591 610.253196501151 27 16.5899700350086 1 4.63957396489301e-05 0.0155425727823916
14 234 Lifr Akt 0.000403304722247795 610.767442037335 27 16.0757244988255 1 6.08592066219105e-05 0.02038783421834
15 276 NoLif Akt 0.000404334343244924 610.767502650423 27 16.0756638857368 1 6.0861154666858e-05 0.0203884868133974
16 241 Lifr Igfr 0.000115383595019422 610.775110756584 27 16.068055779576 1 6.11061703249538e-05 0.0204705670588595
17 283 NoLif Igfr 0.00011538377432933 610.775110803758 27 16.0680557324017 1 6.11061718472916e-05 0.0204705675688427
18 189 Gsk3 mTor -42.5893318331923 611.079589088929 27 15.7635774472307 1 7.17709846050907e-05 0.0240432798427054
19 215 Jak Bmp4r 0.0137196363757733 611.345767060001 27 15.497399476159 1 8.26188395305349e-05 0.0276773112427292
20 214 Jak Bmp4 1 611.642736067823 27 15.2004304683373 1 9.66813791033472e-05 0.0323882619996213

LA9:Lifr->Gsk3

Model residual = 604

Link Extension :
adj_idx from to value residual df Res_delta df_delta pval adj_pval
1 403 Stat3 Bmp4 1 572.876078617921 28 30.8219922886126 1 2.82814514029894e-08 9.44600476859846e-06
2 404 Stat3 Bmp4r 8.13245021756572 572.876088986004 28 30.8219819205297 1 2.82816025043431e-08 9.4460552364506e-06
3 215 Jak Bmp4r 9.36551484046448 576.525518676784 28 27.1725522297493 1 1.86081812292294e-07 6.21513253056262e-05
4 214 Jak Bmp4 1 576.532783064829 28 27.1652878417044 1 1.86782326827561e-07 6.23852971604054e-05
5 152 Fgfr Bmp4r 297.340665110465 582.095106272652 28 21.6029646338822 1 3.35333108014702e-06 0.0011200125807691
6 151 Fgfr Bmp4 1 582.105762712906 28 21.5923081936278 1 3.37201433386891e-06 0.00112625278751222
7 320 Raf Bmp4r 11.8270470999121 583.214400670424 28 20.4836702361097 1 6.01421743351427e-06 0.00200874862279377
8 319 Raf Bmp4 1 583.214995258023 28 20.4830756485111 1 6.01608603745252e-06 0.00200937273650914
9 340 Ras Bmp4 1 583.215295196378 28 20.4827757101555 1 6.01702887148559e-06 0.00200968764307619
10 341 Ras Bmp4r 1 583.285700797687 28 20.4123701088463 1 6.24249802405608e-06 0.00208499434003473
11 275 NoLif Actr 1 584.389561751682 28 19.3085091548517 1 1.11209637640997e-05 0.0037144018972093
12 233 Lifr Actr 1 584.389661932228 28 19.3084089743061 1 1.11215472643478e-05 0.00371459678629217
13 250 Lifr Smad2 -0.212116610255494 584.607072125362 28 19.0909987811717 1 1.24631310476353e-05 0.00416268576991019
14 292 NoLif Smad2 -0.212108033103485 584.607111650283 28 19.0909592562507 1 1.24633891627202e-05 0.00416277198034855
15 136 Fgf4 Igfr -0.0136924775521198 585.362467851911 28 18.3356030546225 1 1.85213296673981e-05 0.00618612410891097
16 418 Stat3 Smad2 0.137439808700106 585.396145396187 28 18.3019255103463 1 1.88516528162319e-05 0.00629645204062145
17 141 Fgf4 Pi3k -0.00813039397930829 585.524959430491 28 18.1731114760425 1 2.01706611024921e-05 0.00673700080823236
18 129 Fgf4 Akt -0.0177917179609664 585.60009932212 28 18.0979715844139 1 2.09824837280603e-05 0.00700814956517214
19 135 Fgf4 Gsk3 -0.000188058181204146 585.882871612964 28 17.8151992935693 1 2.43430879403039e-05 0.0081305913720615
20 260 Mek Fgfr 0.192679681216432 586.701778985757 28 16.9962919207765 1 3.74528915579875e-05 0.0125092657803678

LA10:Jak->Bmp4r

Model residual = 577

Link Extension :
adj_idx from to value residual df Res_delta df_delta pval adj_pval
1 136 Fgf4 Igfr -0.012396447481086 559.030272880804 29 17.4892449017398 1 2.88937594831173e-05 0.00962162190787806
2 141 Fgf4 Pi3k -0.00728552742485347 559.171408434704 29 17.3481093478395 1 3.11207716023887e-05 0.0103632169435954
3 129 Fgf4 Akt -0.0160362834989708 559.234437020547 29 17.2850807619967 1 3.21702796338696e-05 0.0107127031180786
4 135 Fgf4 Gsk3 -0.000146599774087778 559.521830084583 29 16.9976876979603 1 3.74253688779635e-05 0.0124626478363618
5 110 Erk Bmp4r 1.6469473594258 559.838887281016 29 16.6806305015268 1 4.42303044413395e-05 0.0147286913789661
6 109 Erk Bmp4 1 559.892823262074 29 16.6266945204688 1 4.55060139304964e-05 0.0151535026388553
7 257 Mek Bmp4r 5.61869515576583 559.905210098523 29 16.6143076840202 1 4.58041765807327e-05 0.015252790801384
8 256 Mek Bmp4 1 559.951570649855 29 16.5679471326887 1 4.69376573830615e-05 0.0156302399085595
9 260 Mek Fgfr 0.247674458301402 560.212053316471 29 16.3074644660719 1 5.38514044328142e-05 0.0179325176761271
10 113 Erk Fgfr 0.0734811571627518 560.217023394728 29 16.3024943878149 1 5.39928313242344e-05 0.0179796128309701
11 262 Mek Igfr 0.00499004305255553 560.397686954988 29 16.121830827555 1 5.93954127401375e-05 0.0197786724424658
12 115 Erk Igfr 0.00141191682484001 560.398089694532 29 16.1214280880108 1 5.9408044460918e-05 0.0197828788054857
13 267 Mek Pi3k 0.0003206752230825 560.555084991694 29 15.9644327908493 1 6.45437897125456e-05 0.0214930819742777
14 120 Erk Pi3k 8.45351807057001e-05 560.569420898072 29 15.9500968844716 1 6.50344501255118e-05 0.0216564718917954
15 108 Erk Akt 0.000149318325520781 560.604077279719 29 15.9154405028241 1 6.62361529306654e-05 0.0220566389259116
16 255 Mek Akt 0.000640602513307722 560.620169252772 29 15.8993485297714 1 6.68017072702476e-05 0.0222449685209925
17 261 Mek Gsk3 0.000197472821965548 560.674121772617 29 15.8453960099262 1 6.87335600062511e-05 0.0228882754820816
18 114 Erk Gsk3 3.55938257704008e-05 560.691968405884 29 15.8275493766596 1 6.93848770235705e-05 0.023105164048849
19 6 Activin Erk -0.834661255230608 560.786459141758 29 15.7330586407854 1 7.29382282254054e-05 0.02428842999906
20 27 Actr Erk -0.834753819012739 560.786473952003 29 15.7330438305401 1 7.29387992793873e-05 0.024288620160036

XO

Initial-Fit

Model residual = 1604

Link Extension :
adj_idx from to value residual df Res_delta df_delta pval adj_pval
1 218 Jak Fgfr 20.9981411575185 1087.34331547367 17 516.380135442002 1 0 0
2 407 Stat3 Fgfr 31.7189851967562 1087.34331577681 17 516.380135138864 1 0 0
3 216 Jak Erk 0.694604484418286 1259.70107124254 17 344.022379673132 1 0 0
4 405 Stat3 Erk 0.814941886829066 1259.70107125172 17 344.022379663952 1 0 0
5 223 Jak Mek 0.153512756290258 1274.917666653 17 328.805784262674 1 0 0
6 226 Jak Raf 0.153512756290258 1274.917666653 17 328.805784262674 1 0 0
7 227 Jak Ras 0.153512756290258 1274.917666653 17 328.805784262674 1 0 0
8 412 Stat3 Mek 0.169230794744447 1274.91766665487 17 328.805784260799 1 0 0
9 415 Stat3 Raf 0.169230794744447 1274.91766665487 17 328.805784260799 1 0 0
10 416 Stat3 Ras 0.169230794744447 1274.91766665487 17 328.805784260799 1 0 0
11 281 NoLif Fgfr -36.8043300599129 1284.20827336372 17 319.515177551954 1 0 0
12 239 Lifr Fgfr -33.3140786101118 1284.20827336381 17 319.515177551859 1 0 0
13 237 Lifr Erk -1.0966404370305 1307.81404084614 17 295.909410069534 1 0 0
14 279 NoLif Erk -1.09664060257146 1307.81404084681 17 295.909410068864 1 0 0
15 286 NoLif Mek -0.239871652934405 1311.08678085437 17 292.636670061304 1 0 0
16 289 NoLif Raf -0.239871652934405 1311.08678085437 17 292.636670061304 1 0 0
17 290 NoLif Ras -0.239871652934405 1311.08678085437 17 292.636670061304 1 0 0
18 244 Lifr Mek -0.239871665422455 1311.0867808548 17 292.636670060865 1 0 0
19 247 Lifr Raf -0.239871665422455 1311.0867808548 17 292.636670060865 1 0 0
20 248 Lifr Ras -0.239871665422455 1311.0867808548 17 292.636670060865 1 0 0

LA1:Jak -> Fgfr

Model residual = 1064

Link Extension :
adj_idx from to value residual df Res_delta df_delta pval adj_pval
1 268 Mek Raf -5.83511695507381 815.631614262065 18 247.924428670376 1 0 0
2 121 Erk Raf -1.31339551691328 815.631614274121 18 247.924428658321 1 0 0
3 118 Erk Mek -1.3133961412702 815.631614274281 18 247.924428658161 1 0 0
4 122 Erk Ras -1.3133961412702 815.631614274281 18 247.924428658161 1 0 0
5 269 Mek Ras -5.8351805500926 815.631614330806 18 247.924428601636 1 0 0
6 92 Bmp4r Fgfr 99.9999996143922 953.75111984009 19 109.804923092351 2 0 0
7 386 Smad2 Fgfr -0.138087433041223 960.885942419425 18 102.670100513017 1 0 0
8 8 Activin Fgfr -0.107634861881042 960.885942431067 18 102.670100501374 1 0 0
9 29 Actr Fgfr -0.107642013460403 960.885942674455 18 102.670100257986 1 0 0
10 97 Bmp4r Mek 99.999999999432 962.159238790498 19 101.396804141943 2 0 0
11 100 Bmp4r Raf 99.999999999432 962.159238790498 19 101.396804141943 2 0 0
12 101 Bmp4r Ras 99.999999999432 962.159238790498 19 101.396804141943 2 0 0
13 179 Gsk3 Jak 0.10986058964512 962.880760078898 19 100.675282853544 2 0 0
14 180 Gsk3 Lifr 0.10986080686882 962.880760096549 19 100.675282835892 2 0 0
15 90 Bmp4r Erk 0.101155680085491 964.022331185148 19 99.5337117472933 2 0 0
16 384 Smad2 Erk -0.979127856185849 964.487925795937 18 99.0681171365051 1 0 0
17 6 Activin Erk -0.763290332719943 964.487925880594 18 99.0681170518478 1 0 0
18 27 Actr Erk -0.76329033426765 964.487925925433 18 99.0681170070087 1 0 0
19 13 Activin Mek -0.150168153779694 966.972716199464 18 96.5833267329775 1 0 0
20 16 Activin Raf -0.150168153779694 966.972716199464 18 96.5833267329775 1 0 0

LA2:Gsk3->Igfr

Model residual = 971

Link Extension :
adj_idx from to value residual df Res_delta df_delta pval adj_pval
1 268 Mek Raf -5.68048487785159 720.150028354858 20 250.48009389097 1 0 0
2 269 Mek Ras -5.68025951188421 720.15170496036 20 250.478417285468 1 0 0
3 118 Erk Mek -1.30965243655132 720.409297973402 20 250.220824272426 1 0 0
4 122 Erk Ras -1.30965243655132 720.409297973402 20 250.220824272426 1 0 0
5 121 Erk Raf -1.30979470816556 720.725667118639 20 249.904455127189 1 0 0
6 92 Bmp4r Fgfr 9.99999993103222 867.433820816206 21 103.196301429622 2 0 0
7 97 Bmp4r Mek 9.99999867158272 869.583647337226 21 101.046474908602 2 0 0
8 100 Bmp4r Raf 9.99999867158272 869.583647337226 21 101.046474908602 2 0 0
9 101 Bmp4r Ras 9.99999867158272 869.583647337226 21 101.046474908602 2 0 0
10 90 Bmp4r Erk 1.05449863435004 871.564012826834 21 99.0661094189945 2 0 0
11 27 Actr Erk -0.758744726333682 872.346764632357 20 98.2833576134709 1 0 0
12 384 Smad2 Erk -0.973044310674893 872.347291222917 20 98.2828310229108 1 0 0
13 6 Activin Erk -0.758652718543453 872.348908608819 20 98.2812136370086 1 0 0
14 13 Activin Mek -0.151475113899654 875.406405311757 20 95.2237169340711 1 0 0
15 16 Activin Raf -0.151475113899654 875.406405311757 20 95.2237169340711 1 0 0
16 17 Activin Ras -0.151475113899654 875.406405311757 20 95.2237169340711 1 0 0
17 391 Smad2 Mek -0.19613272043099 875.434321883394 20 95.1958003624344 1 0 0
18 394 Smad2 Raf -0.19613272043099 875.434321883394 20 95.1958003624344 1 0 0
19 395 Smad2 Ras -0.19613272043099 875.434321883394 20 95.1958003624344 1 0 0
20 34 Actr Mek -0.158377406543334 875.836265640398 20 94.7938566054301 1 0 0

LA3:Erk->Mek

Model residual = 720

Link Extension :
adj_idx from to value residual df Res_delta df_delta pval adj_pval
1 92 Bmp4r Fgfr 1.00017504349991 611.700315300792 22 108.360117891516 2 0 0
2 97 Bmp4r Mek 100.000000039339 614.975264101 22 105.085169091308 2 0 0
3 100 Bmp4r Raf 100.000000039339 614.975264101 22 105.085169091308 2 0 0
4 101 Bmp4r Ras 100.000000039339 614.975264101 22 105.085169091308 2 0 0
5 395 Smad2 Ras -1.34047605852869 628.213473516405 21 91.8469596759036 1 0 0
6 391 Smad2 Mek -1.34056440965717 628.213476812265 21 91.8469563800433 1 0 0
7 394 Smad2 Raf -1.34037118922177 628.213697011539 21 91.8467361807694 1 0 0
8 34 Actr Mek -1.04471427968771 628.215201432379 21 91.8452317599288 1 0 0
9 38 Actr Ras -1.04471427968771 628.215201432379 21 91.8452317599288 1 0 0
10 37 Actr Raf -1.04471424940284 628.215207421624 21 91.8452257706844 1 0 0
11 17 Activin Ras -1.04496868766343 628.216747935103 21 91.8436852572049 1 0 0
12 13 Activin Mek -1.04496868758615 628.216747937181 21 91.8436852551275 1 0 0
13 16 Activin Raf -1.04496868758615 628.216747937181 21 91.8436852551275 1 0 0
14 29 Actr Fgfr -0.095628702085323 628.980258093207 21 91.0801750991014 1 0 0
15 386 Smad2 Fgfr -0.122711204327267 628.981017715776 21 91.0794154765324 1 0 0
16 8 Activin Fgfr -0.0955736930359601 628.981707654339 21 91.0787255379689 1 0 0
17 96 Bmp4r Lifr 1.41042555033286 636.525329768387 22 83.5351034239216 2 0 0
18 95 Bmp4r Jak 99.9999999991175 637.462042126243 22 82.5983910660655 2 0 0
19 103 Bmp4r Smad2 1.00165261367737 638.747808236162 22 81.3126249561459 2 0 0
20 86 Bmp4r Actr 1.00165261367736 638.747808236176 22 81.3126249561324 2 0 0

LA4:Bmp4r->Fgfr

Model residual = 611

Link Extension :
adj_idx from to value residual df Res_delta df_delta pval adj_pval
1 86 Bmp4r Actr 5.86687019434621 530.138061090517 23 81.3425443119849 1 0 0
2 103 Bmp4r Smad2 5.86688396987027 530.138065632416 23 81.3425397700859 1 0 0
3 219 Jak Gsk3 0.0972369985413909 547.331781134442 23 64.1488242680596 1 1.11022302462516e-15 3.76365605347929e-13
4 408 Stat3 Gsk3 0.116437723891935 547.331783336583 23 64.148822065918 1 1.11022302462516e-15 3.76365605347929e-13
5 414 Stat3 Pi3k 0.00278195021560732 550.102566625797 23 61.3780387767044 1 4.66293670342566e-15 1.5807355424613e-12
6 225 Jak Pi3k 0.00237150099487695 550.112700011199 23 61.3679053913029 1 4.77395900588817e-15 1.61837210299609e-12
7 402 Stat3 Akt 0.000346292138367275 550.159597947644 23 61.3210074548573 1 4.88498130835069e-15 1.65600866353088e-12
8 409 Stat3 Igfr 0.00267507825783261 550.171301219393 23 61.3093041831083 1 4.88498130835069e-15 1.65600866353088e-12
9 220 Jak Igfr 0.00212368313237165 550.179742880404 23 61.3008625220972 1 4.88498130835069e-15 1.65600866353088e-12
10 213 Jak Akt 0.00027839697601006 550.180441768978 23 61.3001636335234 1 4.88498130835069e-15 1.65600866353088e-12
11 317 Raf Actr 0.995293695761167 551.201394840101 23 60.2792105624009 1 8.21565038222616e-15 2.78510547957467e-12
12 334 Raf Smad2 0.995293695761167 551.201394840101 23 60.2792105624009 1 8.21565038222616e-15 2.78510547957467e-12
13 338 Ras Actr 0.995293695761167 551.201394840101 23 60.2792105624009 1 8.21565038222616e-15 2.78510547957467e-12
14 355 Ras Smad2 0.995293695761167 551.201394840101 23 60.2792105624009 1 8.21565038222616e-15 2.78510547957467e-12
15 149 Fgfr Actr 1 551.261964847594 23 60.218640554908 1 8.43769498715119e-15 2.86037860064425e-12
16 166 Fgfr Smad2 1 551.261964847594 23 60.218640554908 1 8.43769498715119e-15 2.86037860064425e-12
17 254 Mek Actr 0.593840281484033 552.874753568515 23 58.6058518339868 1 1.93178806284777e-14 6.54876153305394e-12
18 271 Mek Smad2 0.593895601175709 552.876435578234 23 58.6041698242677 1 1.93178806284777e-14 6.54876153305394e-12
19 107 Erk Actr 0.126701455011672 552.878653223665 23 58.6019521788369 1 1.93178806284777e-14 6.54876153305394e-12
20 124 Erk Smad2 0.126626186957925 552.881245925014 23 58.5993594774873 1 1.93178806284777e-14 6.54876153305394e-12

LA5:Jak ->Gsk3

Model residual = 547

Link Extension :
adj_idx from to value residual df Res_delta df_delta pval adj_pval
1 103 Bmp4r Smad2 0.184039407308206 465.989068855463 24 81.3427112952518 1 0 0
2 86 Bmp4r Actr 0.18401069929792 465.989068858964 24 81.342711291751 1 0 0
3 359 Smad1 Actr 1 465.989069002156 24 81.3427111485585 1 0 0
4 376 Smad1 Smad2 1 465.989069005101 24 81.342711145614 1 0 0
5 166 Fgfr Smad2 0.787412501709583 487.061034123738 24 60.2707460269772 1 8.21565038222616e-15 2.77688982919244e-12
6 338 Ras Actr 0.787396035446579 487.06103412831 24 60.2707460224054 1 8.21565038222616e-15 2.77688982919244e-12
7 334 Raf Smad2 0.787401177145844 487.061034129885 24 60.2707460208296 1 8.21565038222616e-15 2.77688982919244e-12
8 317 Raf Actr 0.787447609308935 487.061034156285 24 60.2707459944302 1 8.21565038222616e-15 2.77688982919244e-12
9 149 Fgfr Actr 0.787387354758698 487.061034164812 24 60.2707459859027 1 8.21565038222616e-15 2.77688982919244e-12
10 355 Ras Smad2 0.787439992189182 487.061034172604 24 60.2707459781111 1 8.21565038222616e-15 2.77688982919244e-12
11 254 Mek Actr 0.543844924532893 493.382476011324 24 53.9493041393909 1 2.05724326463042e-13 6.95348223445082e-11
12 124 Erk Smad2 0.123251777854743 493.382476050697 24 53.9493041000184 1 2.05724326463042e-13 6.95348223445082e-11
13 107 Erk Actr 0.123252069043532 493.382476054152 24 53.9493040965632 1 2.05724326463042e-13 6.95348223445082e-11
14 271 Mek Smad2 0.543845016513122 493.382476119721 24 53.9493040309943 1 2.05724326463042e-13 6.95348223445082e-11
15 180 Gsk3 Lifr 0.254069080523393 498.901017903447 24 48.4307622472683 1 3.42159633959227e-12 1.15649956278219e-09
16 179 Gsk3 Jak 0.2540693850344 498.901018150175 24 48.4307620005403 1 3.42159633959227e-12 1.15649956278219e-09
17 200 Igfr Jak 0.394644138994172 502.069365669424 24 45.2624144812914 1 1.72324376990218e-11 5.82456394226937e-09
18 201 Igfr Lifr 0.394606918882979 502.069365777655 24 45.2624143730599 1 1.72324376990218e-11 5.82456394226937e-09
19 386 Smad2 Fgfr -0.119229271726118 502.642865744755 24 44.6889144059604 1 2.30960806035796e-11 7.8064752440099e-09
20 29 Actr Fgfr -0.0929468005033651 502.642865761317 24 44.6889143893981 1 2.30960806035796e-11 7.8064752440099e-09

LA6:Bmp4r->Smad2

Model residual = 466

Link Extension :
adj_idx from to value residual df Res_delta df_delta pval adj_pval
1 179 Gsk3 Jak 0.254068951082065 417.558306756105 25 48.4307620112604 1 3.42159633959227e-12 1.15307796644259e-09
2 180 Gsk3 Lifr 0.254071104301913 417.558306834712 25 48.4307619326527 1 3.42159633959227e-12 1.15307796644259e-09
3 201 Igfr Lifr 0.394542656867191 420.726654719223 25 45.2624140481417 1 1.72324376990218e-11 5.80733150457035e-09
4 200 Igfr Jak 0.3944863064986 420.726655148809 25 45.2624136185564 1 1.72324376990218e-11 5.80733150457035e-09
5 29 Actr Fgfr -0.092945624966265 421.300154446345 25 44.68891432102 1 2.30960806035796e-11 7.78337916340632e-09
6 386 Smad2 Fgfr -0.099438325552686 421.300154450011 25 44.6889143173542 1 2.30960806035796e-11 7.78337916340632e-09
7 8 Activin Fgfr -0.092947010470707 421.300154473776 25 44.6889142935888 1 2.30960806035796e-11 7.78337916340632e-09
8 382 Smad2 Bmp4 1 421.30133971483 25 44.6877290525346 1 2.31100694136899e-11 7.7880933924135e-09
9 383 Smad2 Bmp4r -6.6538715882205e-05 421.301339804655 25 44.6877289627099 1 2.31100694136899e-11 7.7880933924135e-09
10 26 Actr Bmp4r -0.00014014367166331 421.302820869133 25 44.6862478982321 1 2.3127610937479e-11 7.79400488593042e-09
11 5 Activin Bmp4r -0.000140133205069961 421.302821657184 25 44.6862471101813 1 2.3127610937479e-11 7.79400488593042e-09
12 4 Activin Bmp4 -0.000140133538825714 421.302821759723 25 44.6862470076421 1 2.3127610937479e-11 7.79400488593042e-09
13 25 Actr Bmp4 -0.000140135825763944 421.302822364256 25 44.686246403109 1 2.3127610937479e-11 7.79400488593042e-09
14 394 Smad2 Raf -0.823997308105129 422.178358227844 25 43.8107105395209 1 3.61719543207073e-11 1.21899486060784e-08
15 391 Smad2 Mek -0.823997100934504 422.178358228294 25 43.8107105390706 1 3.61719543207073e-11 1.21899486060784e-08
16 395 Smad2 Ras -0.823996874322976 422.178358231202 25 43.8107105361634 1 3.61719543207073e-11 1.21899486060784e-08
17 37 Actr Raf -0.766283034702303 422.577980657324 25 43.4110881100414 1 4.43667325100705e-11 1.49515888558938e-08
18 38 Actr Ras -0.766283034702303 422.577980657324 25 43.4110881100414 1 4.43667325100705e-11 1.49515888558938e-08
19 34 Actr Mek -0.766283054935296 422.57798066996 25 43.4110880974046 1 4.43667325100705e-11 1.49515888558938e-08
20 17 Activin Ras -0.766283484192922 422.577980711525 25 43.4110880558399 1 4.43667325100705e-11 1.49515888558938e-08

LA7:Actr->Ras

Model residual = 423

Link Extension :
adj_idx from to value residual df Res_delta df_delta pval adj_pval
1 180 Gsk3 Lifr 0.204449789427288 386.280620890445 26 36.2973595765252 1 1.69393199467294e-09 5.69161150210108e-07
2 179 Gsk3 Jak 0.204451759095846 386.280621082363 26 36.297359384607 1 1.69393221671754e-09 5.69161224817093e-07
3 188 Gsk3 Stat3 0.160457470553098 388.755973945851 26 33.8220065211191 1 6.03918448582874e-09 2.02916598723846e-06
4 200 Igfr Jak 0.329294397141902 390.071887880546 26 32.5060925864243 1 1.18819449834717e-08 3.99233351444649e-06
5 201 Igfr Lifr 0.32928440535087 390.071887918402 26 32.5060925485674 1 1.18819452055163e-08 3.99233358905348e-06
6 209 Igfr Stat3 0.231612782637007 394.043515363579 26 28.534465103391 1 9.20453719910341e-08 3.09272449889875e-05
7 234 Lifr Akt 0.0462196227783465 396.116365997349 26 26.4616144696204 1 2.68827251015402e-07 9.03259563411751e-05
8 276 NoLif Akt 0.0462165165836588 396.116366081835 26 26.4616143851351 1 2.68827262783766e-07 9.03259602953454e-05
9 241 Lifr Igfr 0.135793139520361 396.668918218988 26 25.9090622479821 1 3.57885072022057e-07 0.000120249384199411
10 283 NoLif Igfr 0.135782917338045 396.668918232099 26 25.9090622348712 1 3.57885074353526e-07 0.000120249384982785
11 246 Lifr Pi3k 1.28992919217763 396.763764952033 26 25.8142155149364 1 3.75909642080785e-07 0.000126305639739144
12 288 NoLif Pi3k 1.28994875016742 396.763764969256 26 25.814215497714 1 3.75909645522476e-07 0.000126305640895552
13 282 NoLif Gsk3 0.122362305233547 396.92669794267 26 25.6512825242995 1 4.09023556247057e-07 0.000137431914899011
14 240 Lifr Gsk3 0.122360298845118 396.926697951235 26 25.6512825157348 1 4.09023558134436e-07 0.00013743191553317
15 432 mTor Lifr 0.469152832603995 398.054726959083 26 24.5232535078864 1 7.34184159245643e-07 0.000246685877506536
16 305 Pi3k Jak 0.017433244009084 398.054727206694 26 24.5232532602757 1 7.341842536146e-07 0.000246685909214506
17 306 Pi3k Lifr 0.017431204338884 398.054727217841 26 24.5232532491284 1 7.34184257833448e-07 0.000246685910632039
18 53 Akt Jak 0.570660129762602 398.054727401473 26 24.5232530654965 1 7.34184327777498e-07 0.000246685934133239
19 431 mTor Jak 0.469146155189099 398.054728085877 26 24.5232523810931 1 7.34184588568887e-07 0.000246686021759146
20 54 Akt Lifr 0.57064380819813 398.054728096347 26 24.5232523706227 1 7.3418459256569e-07 0.000246686023102072

LA8:Gsk3->Stat3

Model residual = 389

Link Extension :
adj_idx from to value residual df Res_delta df_delta pval adj_pval
1 282 NoLif Gsk3 0.340161211829361 363.043453111378 27 25.7125207094361 1 3.96247904266289e-07 0.000132743047929207
2 240 Lifr Gsk3 0.340156823652642 363.043453403628 27 25.7125204171865 1 3.96247964329355e-07 0.000132743068050334
3 234 Lifr Akt 0.0864753723916127 365.592813384858 27 23.1631604359559 1 1.48821191259252e-06 0.000498550990718494
4 276 NoLif Akt 0.0864708725186882 365.592813858268 27 23.1631599625465 1 1.48821227896612e-06 0.00049855111345365
5 404 Stat3 Bmp4r 5.14175535607917 365.829402244055 27 22.9265715767592 1 1.6830907973997e-06 0.0005638354171289
6 403 Stat3 Bmp4 1 365.829405138198 27 22.9265686826164 1 1.68309333148375e-06 0.000563836266047056
7 215 Jak Bmp4r 4.83051262964478 366.702300375898 27 22.0536734449161 1 2.65131796972629e-06 0.000888191519858307
8 214 Jak Bmp4 1 366.702300553851 27 22.0536732669633 1 2.65131821552966e-06 0.000888191602202436
9 241 Lifr Igfr 0.27820929917877 367.213569958621 27 21.5424038621928 1 3.46090791081277e-06 0.00115940415012228
10 283 NoLif Igfr 0.278129879717177 367.213570101492 27 21.5424037193217 1 3.46090816860656e-06 0.0011594042364832
11 288 NoLif Pi3k 3.55459249358911 367.302683571713 27 21.4532902491011 1 3.62553373389751e-06 0.00121455380085567
12 246 Lifr Pi3k 3.55867955091611 367.302683590274 27 21.4532902305399 1 3.62553376898056e-06 0.00121455381260849
13 401 Stat3 Actr 1 369.092911753531 27 19.6630620672835 1 9.2369721953478e-06 0.00309438568544151
14 212 Jak Actr 1 369.108604978772 27 19.6473688420419 1 9.31314655272519e-06 0.00311990409516294
15 418 Stat3 Smad2 0.123285165097414 369.131846240073 27 19.6241275807416 1 9.4271190844708e-06 0.00315808489329772
16 229 Jak Smad2 0.129255806208675 369.295363793503 27 19.4606100273112 1 1.0269577858657e-05 0.00344030858265009
17 136 Fgf4 Igfr -0.302239278705564 369.939930009162 27 18.8160438116519 1 1.43951114580654e-05 0.00482236233845191
18 141 Fgf4 Pi3k -3.84633626774211 370.137591391957 27 18.6183824288571 1 1.59673456850973e-05 0.0053490608045076
19 244 Lifr Mek -0.968537585229697 370.900682116607 27 17.8552917042072 1 2.38355523596301e-05 0.00798491004047608
20 286 NoLif Mek -0.968537514999281 370.900682123461 27 17.8552916973528 1 2.38355524455613e-05 0.00798491006926304

LA9:Lifr->Gsk3

Model residual = 363

Link Extension :
adj_idx from to value residual df Res_delta df_delta pval adj_pval
1 404 Stat3 Bmp4r 4.42475341890749 340.982857447563 28 22.0605956844269 1 2.64177383713093e-06 0.000882352461601731
2 403 Stat3 Bmp4 1 340.982857618394 28 22.0605955135965 1 2.64177407227617e-06 0.000882352540140241
3 215 Jak Bmp4r 52.355777048759 341.656398246847 28 21.3870548851436 1 3.75296587085128e-06 0.00125349060086433
4 214 Jak Bmp4 1 341.656400962345 28 21.3870521696449 1 3.75297118637707e-06 0.00125349237624994
5 401 Stat3 Actr 1 343.449501648668 28 19.593951483322 1 9.57719144634162e-06 0.0031987819430781
6 418 Stat3 Smad2 0.122583078907248 343.554946393052 28 19.4885067389387 1 1.0120680649317e-05 0.00338030733687188
7 62 Akt Stat3 -3.6354949850077 344.145773576097 28 18.8976795558937 1 1.37920329837948e-05 0.00460653901658746
8 314 Pi3k Stat3 -0.104722350512355 344.145773582876 28 18.8976795491148 1 1.37920330328667e-05 0.00460653903297748
9 440 mTor Stat3 -3.00146504106831 344.145773792024 28 18.897679339966 1 1.37920345449905e-05 0.00460653953802683
10 229 Jak Smad2 0.192179763329023 344.457364986238 28 18.5860881457528 1 1.62401393908329e-05 0.00542420655653819
11 212 Jak Actr 1 344.497041593409 28 18.5464115385814 1 1.65817100210575e-05 0.00553829114703321
12 136 Fgf4 Igfr -0.265988052412529 347.886285664377 28 15.1571674676137 1 9.89220773610633e-05 0.0330399738385951
13 141 Fgf4 Pi3k -2.77746740523667 348.116389958882 28 14.9270631731086 1 0.0001117483662052 0.0373239543125368
14 152 Fgfr Bmp4r 15.7374492089758 348.271562471386 28 14.7718906606048 1 0.000121330702603228 0.0405244546694782
15 151 Fgfr Bmp4 1 348.27156264423 28 14.7718904877607 1 0.000121330713724888 0.0405244583841126
16 135 Fgf4 Gsk3 -0.14538143998535 348.579784064105 28 14.4636690678858 1 0.000142889094074339 0.0477249574208292
17 320 Raf Bmp4r 0.0171822060206794 349.438632518151 28 13.6048206138391 1 0.000225605458112343 0.0753522230095226
18 340 Ras Bmp4 1 349.438636739997 28 13.6048163919932 1 0.000225605965473497 0.075352392468148
19 319 Raf Bmp4 1 349.43863677331 28 13.6048163586806 1 0.00022560596947685 0.0753523938052679
20 341 Ras Bmp4r 1 349.438644358464 28 13.6048087735259 1 0.000225606881027351 0.0753526982631352

LA10:Jak->Bmp4r

Model residual = 342

Link Extension :
adj_idx from to value residual df Res_delta df_delta pval adj_pval
1 314 Pi3k Stat3 -0.0376082804084924 324.184135168756 29 17.4722599767638 1 2.9153056752107e-05 0.00970796789845163
2 62 Akt Stat3 -2.97929495127255 324.18413520201 29 17.4722599435098 1 2.91530572621435e-05 0.00970796806829378
3 440 mTor Stat3 -2.4604910805264 324.184135647864 29 17.4722594976567 1 2.91530640992299e-05 0.00970797034504356
4 136 Fgf4 Igfr -0.267309926001727 326.540300659235 29 15.1160944862853 1 0.000101097695986208 0.0336655327634073
5 141 Fgf4 Pi3k -33.576277771911 326.759709515117 29 14.8966856304035 1 0.000113562331586325 0.0378162564182462
6 135 Fgf4 Gsk3 -0.145791901886765 327.247267466072 29 14.4091276794483 1 0.000147087633789567 0.0489801820519258
7 405 Stat3 Erk 0.509670772028657 328.581341144008 29 13.0750540015117 1 0.000299254591787479 0.0996517790652305
8 239 Lifr Fgfr -0.0847281686137454 328.607271046939 29 13.049124098581 1 0.000303426277666219 0.101040950462851
9 281 NoLif Fgfr -0.0847016937219506 328.607271571753 29 13.0491235737671 1 0.00030342636269054 0.10104097877595
10 248 Lifr Ras -0.891341343217465 328.650282392531 29 13.0061127529893 1 0.000310475788542597 0.103388437584685
11 290 NoLif Ras -0.891340947582484 328.650282574366 29 13.0061125711541 1 0.000310475818691591 0.1033884476243
12 289 NoLif Raf -0.89134064776854 328.650283135223 29 13.0061120102972 1 0.000310475911683872 0.103388478590729
13 244 Lifr Mek -0.891347448540436 328.650283237858 29 13.0061119076618 1 0.000310475928701259 0.103388484257519
14 247 Lifr Raf -0.891347804902039 328.650283292683 29 13.0061118528369 1 0.000310475937791432 0.103388487284547
15 286 NoLif Mek -0.891346664414445 328.65028330654 29 13.0061118389801 1 0.000310475940088928 0.103388488049613
16 129 Fgf4 Akt -0.0574349970233671 328.968238057895 29 12.688157087625 1 0.000367978765073218 0.122536928769382
17 137 Fgf4 Jak -0.0904530024566078 329.045312261902 29 12.6110828836178 1 0.000383466286562051 0.127694273425163
18 142 Fgf4 Raf 2.87447197758744 329.138739961138 29 12.5176551843819 1 0.000403124490265139 0.134240455258291
19 139 Fgf4 Mek 2.87448759372652 329.138867144109 29 12.5175280014111 1 0.000403151932417023 0.134249593494869
20 143 Fgf4 Ras 2.87473941728419 329.139324531587 29 12.5170706139334 1 0.000403250638066455 0.13428246247613

Summary

Links Added and Residuals

Model_iteration Links res_p_01_XX res_p_01_XO
1 Init Init Network 2056.3 1603.72
2 1 Jak->Fgfr 1515 1063.56
3 2 Gsk3->Igfr 970.96 970.63
4 3 Erk->Mek 932.14 720.06
5 4 Bmp4r->Fgfr 798.29 611.48
6 5 Jak->Gsk3 737.94 547.33
7 6 Bmp4r->Smad2 691.87 465.99
8 7 Actr->Ras 645.08 422.58
9 8 Gsk3->Stat3 626.84 388.76
10 9 Lifr->Gsk3 603.7 363.04
11 10 Jak->Bmp4r 576.52 341.66